6nhz

<StructureSection load='6nhz' size='340' side='right' caption='[[6nhz]], [[Resolution|resolution]] 1.80&Aring;' scene=''>

<table><tr><td colspan='2'>[[6nhz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHZ FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6nhx|6nhx]]</td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ERS027656_00724 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>

<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </span></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhz OCA], [http://pdbe.org/6nhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nhz RCSB], [http://www.ebi.ac.uk/pdbsum/6nhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhz ProSAT]</span></td></tr>

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== Publication Abstract from PubMed ==

DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD(+) to form a covalent ligase-(lysyl-Nzeta)-AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide (NMN). In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase (NTase) domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.6 A resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to non-homologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 A), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD*ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg(2+) that engages the ATP alpha phosphate and a second metal that bridges the ATP beta and gamma phosphates.

 

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== References ==

[[Category: Goldgur, Y]]

[[Category: Shuman, S]]

[[Category: Unciuleac, M]]

[[Category: Dna ligase]]

[[Category: Ligase]]